


Aye, Captain.

by Redrobinr



Category: The Maze Runner Series - James Dashner
Genre: Aged-Up Character(s), Alcohol, Alternate Universe - Pirate, Alternative Lifestyles, Assumptions, Awesome Minho (Maze Runner), Bad Decisions, Badass Newt (Maze Runner), Bisexual Thomas (Maze Runner), Bottom Minho (Maze Runner), Canonical Character Death, Character Death, Dom/sub, Dominant Thomas (Maze Runner), Everyone Has Issues, Explicit Language, F/F, Flirting, Freeform, Hate to Love, I Ship It, Implied Relationships, Implied/Referenced Child Abuse, Implied/Referenced Rape/Non-con, Implied/Referenced Sex, Love/Hate, M/M, Mild S&M, Minor Character Death, Minor Character(s), My First Work in This Fandom, Not Canon Compliant, POV Alternating, Pirates, Relationship(s), Royalty, Sarcasm, Sassy Minho, Sassy Newt (Maze Runner), Slow Build, Slow Burn, Slow Romance, Swearing, Swords, Teresa Agnes and Thomas (Maze Runner) are Twins, Threats of Violence, Top Newt (Maze Runner)
Language: English
Status: In-Progress
Published: 2019-10-12
Updated: 2019-10-13
Packaged: 2020-12-09 18:54:16
Rating: Mature
Warnings: Graphic Depictions Of Violence, Major Character Death, Rape/Non-Con
Chapters: 2
Words: 4,495
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/20999681
Author URL: https://archiveofourown.org/users/Redrobinr/pseuds/Redrobinr
Summary: Thomas Murphy is the infamous pirate captain of The Glade. His crew, known as The Gladers, is classed as a close knit family.Minho Park, on the other hand, is the crown prince of Astana (not that he acts like it), though he'd rather not be.Two very different sides of society meeting upon the neutral grounds of the ocean. What could possibly go wrong?





	1. Prologue

The port was rather full today. That was the first thing the 22 year old noted. The second thing he noted was how everyone split apart like water around a rock as he walked, making room for him. He chuckled lightly when he saw the fear and respect in their eyes. He **thrived** off of those looks.

  
“Tommy,” he stopped upon hearing the nickname and looked at the blonde with a raised brow, “don’t get too cocky. It’ll be the end of you.”

  
Thomas nodded quietly and smiled, which seemed to be both dark and reassuring.

  
“I know, Newt. Go get some food or relax, okay? We’re not gonna be at Bredon long.”

  
Newton huffed and rolled his eyes, giving Thomas a gentle punch on the arm and a ‘later’ before he left, catching up to the other crewmates. He watched the pale form clad in a loose beige shirt disappear with the rest of the crew.

  
“Now… Time to get myself a drink…”

* * *

  
Upon entering the pub, Thomas could feel the tense silence that fell over the room. He walked over to the bar, smiled at the keep – who immediately walked over to him, ignoring her other customers - and leaned on the wooden surface. He sent a wink her way as he spoke.

  
“Gimme something strong, love.”

  
A blush and nod from her and soon there was a mug of strong liquor in front of him. He downed it rather quickly, placed down the correct amount of money and left with a smug grin as he heard them talking about him once he was out the door.

  
He met up with Newt on the dock, who promptly sighed when he picked up on the alcohol, and boarded _The Glade_. Swift greetings from the crew and an equally quick response from Thomas then the ship was out of dock. Thomas watched with intrigue as Gally was scolding a young, curly-haired and podgy boy who had stowed himself on board; he cleared his throat once nearby and both pairs of eyes – scared brown and stern grey – looked straight at him.

  
“Kid thought it’d be smart to stowaway, Thomas,” Gally spoke straight away when Thomas raised a brow and met his gaze, “what’d you want to do?”

  
The boy seemed desperate when he looked at Thomas and soon he noticed why. He gently pulled the shirt collar aside to see welts, bruises and burn marks on the child's skin.

  
“Why’d you come aboard, kid?” Thomas asked calmly, and he almost felt sorry for the boy’s throat when he heard the broken sounding voice respond.

  
“Because I didn’t want to found by my dad...”

  
Thomas was silent at the response and he caught Gally's expression soften instantly when he picked up on the situation. Thomas spoke again, looking at the boy.

  
“He did this, didn’t he?”

  
No verbal response, just a sharp nod. Thomas reared back and exchanged a look with Gally, who clearly disliked the whole thing. His eyes went back to those terrified brown ones.

  
“What’s your name, kid?”

  
“Chuck.”

  
“We can’t keep you on board, y’know, Chuck,” Thomas’s brows scrunched up when he saw Chuck deflate at his words, “but we can take you to our home on land. I’m sure my sister and her partner would love the company. You can officially join our crew when you’re a little older.”

  
The boy brightened up and smiled slightly and Gally just sighed at Thomas’s softness. Thomas ignored the other man and took Chuck's hand to show him around. The whole crew were more than happy with Thomas’s decision, and soon he was in the medical care of Clint and Jeff. Chuck seemed even more grateful when Frypan gave him some food he'd recently made.

  
By the time they arrived at the crew’s home on land, Chuck looked much better. He had been treated carefully and he had a healthier shine in his eyes. When Thomas knocked on the door of his sister’s, Teresa’s, home and explained the situation she openly let him in. Teresa’s girlfriend, Brenda, was content with letting the boy stay so long as he helped out with the chores, which Chuck agreed with quickly.

  
Needless to say, Thomas felt rather relieved when they left the cove and were back on the waves and he made sure to share his pleasant mood with Newt, much to the crew's annoyance.

* * *

  
“I’m just saying, could you guys be a _little_ quieter next time?” Those pleading words made Thomas chuckle and he found himself grinning like a lunatic when he heard Newt's remark to them.

  
“Be louder next time? Alright, Zart.”

  
_“No!”_

  
A loud laugh from Newt then a yell of frustration came from Zart as the blonde man left to go below deck.

  
Winston walked over to Thomas with a shake of his head and a chuckle. The two openly conversed before Winston gestured to something on the horizon. Upon focusing on it, Thomas realised it was a rather large, exotic looking ship. Very well crafted as well.

  
“It’s headed this way,” Winston pointed out and Thomas nodded with a conniving smirk on his lips, “looks pretty well-stocked as well…”

  
“Aye, that it does, Winston,” he leaned on the rails of his ship and gestured for Winston to hand over the handheld telescope he always had on him. Upon feeling the familiar weight in his palm, he looked through the glass and only widened his smirk, “it’s a royal merchant ship as well. Perfect looting opportunity.”

  
He removed the telescope from his eye and looked at his crewmate, who seemed to be ready to respond to an order. A simple jerk of his head, and Winston was down the stairs and getting everyone ready for the attack. There was no way in hell that Thomas was letting this one escape.

* * *

  
Dark eyes were focused on the paper in front of them on the mahogany table. A hand absently fiddling with the red jewel earring dangling beside his left eye. He pulled his lower lip inwards as he read the map and distinguished where they were. They were in pirate territory now.

  
“Prince Minho, there’s a ship approaching ours.”

  
Minho's eyes looked up at the old sailor in front of him. He pushed himself from the desk and followed the man to the bow of the ship. His eyes narrowed when he saw the approaching vessel and the moment he saw the flag, he panicked. Since he found out about the trip, the 23-year old read all about the different flags and ships and he recognized that one to be a pirate’s flag.

  
“We should change course. That’s a pirate ship.”

  
The sailor's eyes widened upon the words of the prince, and when he looked at the ship again, he paled slightly as he mentally confirmed the young man's words. They were ill-prepared for a pirate attack and he had sworn to keep both the cargo and the prince safe. He quickly approached the ship's wheel and prepared to change course, though he apparently did it too late. There was a loud crash as the ship was rammed and soon the boarding occurred. It also seemed he had been too focused on the attack, as the prince was now out of sight.

  
Minho had rushed into his room the moment he saw the pirates were close and fast approaching. He lost balance momentarily as he heard the telltale sound of a ramming as the ship quaked and grabbed his blades. He checked his dagger was sharp enough before he slotted it in the sheath on his belt. The ringing of metal reached his ears the moment he stepped outside onto the deck and he quickly got involved in the fight for the ship.

  
He parried a cutlass that came his way and found himself locked in a battle with the man that had attacked him. He found himself reaching a stalemate with the blade, so he changed his tactic and swept the pirate's legs out from under him. As soon as the other fell, he disarmed him and finished the battle with a smooth strike of his basket-hilted sword to the chest. It seemed that was a bad move though, as he was quickly attacked by one of the other pirates. He just mentally thanked his mentor for teaching him how to dual-wield swords as he was attacked on another side. A quick push on the right and an elbow to the left and both pirates had been pushed away from him, the space a necessary blessing as he incapacitated one and struck the other down with the curved blade. Minho felt eyes boring into his back and stopped to look in the direction he guessed the gaze was originating from. He soon met the brown eyes of a dark-haired man, who Minho unfortunately recognised. _Captain Murphy._

* * *

  
Thomas had been watching the fight carefully and found his attention being pulled to the region near the bow of the merchant ship. There he saw a man with naturally black swept up hair, with tanned skin who was very well-dressed.

  
At first, he paid no attention to the fighting, just the tailored white silk shirt and black trousers that went into some very interesting knee-high brown leather boots that could definitely sell for plenty. Then he watched the man's footwork and his attention went straight up to the body to the blades he was wielding with clear refinement. A well-executed spin allowed for him to parry an attack from the left with precision then he tilted his right wrist just so and caught the attack from the right and used that precious wasted second on his crewmate's end to cut his shins and kick him down.

  
Whoever this man was, he knew how to fight and Thomas soon found himself heading straight to the well-dressed individual. He saw the male quickly knock down another of Thomas’s crew before he was stopped by Thomas’s sabre blade angled at his throat. The one who had been fighting this individual, who Thomas realised was Ben, quickly scurried away to allow his captain to take over.

  
“Thomas Murphy,” Thomas was roped into that smooth voice and found himself wanting to hear this man say his name more. He smirked at his opponent, who frowned lightly and knocked his blade from his neck, “how fucking great.”

  
“Seems like you don’t like me,” Thomas remarked and quickly blocked a strike from the other, “shame. I was hoping we could get along.”

  
The swordsman scoffed and narrowed his eyes as he watched Thomas’s movements carefully.

  
“Not a chance,” another strike, one that Thomas probably could’ve knocked away if he hadn’t been staring at the guy's figure, but damn he couldn’t help it. The guy had one hell of a body if that tight fitting clothing had anything to say, “shouldn’t you pay attention to your opponent, _Captain?”_

  
“I’d much rather pay attention to you in a different way, to be entirely honest with you.”

  
A groan from the man demonstrated that he did not appreciate the comment. Then another strike, a sweeping kick behind the knee that lurched Thomas forward. Thomas chuckled. He fought dirty as well, it seemed.

  
“Do us both a favour and shut it.” The young man smiled mockingly then let out a small sound of shock when he saw Thomas lunge up and tug him down by the collar, putting them in very close proximity to each other.

  
“Only if you ask nicely.”

  
“How about no?” A smirk on pink lips and then there was a sharp pang in Thomas’s groin. A glance down revealed a knee pressing down harshly and he had to admit, that really shouldn’t of turned him on as much as it did.

  
“Playing hard to get?” He quickly knocked the dark-eyed man off him and stood, sword tip pressed on the other’s chest and soon there was a look of irritation on the male’s face before his blade was knocked out of his hand and pinned to the ground by the cutlass his enemy had borrowed.

  
Thomas had been startled and he showed that, an amateur mistake on his part. Then he was holding the wrist still containing the basket-hilted sword in hand to prevent the steel from getting any closer. He angled his hand just right, and a small cry of pain came from the man as he let go of the handle and let the sword clatter against the wooden deck.

  
A hiss of pain came from Thomas as he felt cold metal tear into his shoulder. He realised much too soon that his opponent had a third weapon, a sharpened dagger, with – from what he could see – an intricately decorated leather handle. He refused to let go of the wrist he held captive and quickly found himself wrestling with the other to get some distance between him and the weapon. He thanked Gally mentally for always sparring with him as he managed to overpower him and press his own blade against his neck. A knee in-between his legs and his body pressed into the swordsman prevented him from moving at all.

  
“Now if only we were like this on a bed.”

  
A growl came from the tanned man and just as he was about to speak, a cry came from an elder sailor.

  
“We surrender! We surrender. Please don’t harm the prince!”

  
Coal eyes widened as the pinned male looked directly at the sailor and Thomas couldn’t help but smirk at the shocked figure beneath him.

  
“A prince? Must be my lucky day.”

  
“Must be…” the prince muttered bitterly as he let out a huff of exasperation. That was when Thomas realised the merchants were not moving at all, just focused on the young man currently beneath him.

  
“Gentlemen, take what you can and kill the crew.”

  
“No!”

  
He heard the dread in the prince’s shout at his words as he saw his crew grin maniacally and start killing the unresisting merchants. He could feel the male beneath him writhe, trying fruitlessly to get away and save the crew while keeping his neck away from the blade and Thomas was relishing in it. He met Newt’s gaze, and the moment the blonde jerked his head in the direction of the prince, Thomas grinned, removed the blade from his neck and tugged the male up. He made sure he had a tight grasp on him as he hauled the royal over his shoulder and started heading back to the ship, keeping him there despite the fact that he was struggling.

  
By the time they were halfway across the boarding planks, he felt his captive stop and just give in. Over the screams of the merchants and the sound of swords tearing flesh and clothes, he heard the defeated sound from the lips of the royal and the rustle of his black cotton jacket as the other just pressed his face into the material to stop himself from seeing the massacre as they returned to the captain's quarters of _The Glade_.


	2. Chapter 1

**Summary for the Chapter:**

> In which Minho attempts escape and Thomas settles on what he wants to do with the prince.

Minho remained silent as he heard the captain move from the bed. He kept his eyes facing anywhere else but the other man, even as Thomas tried to direct his gaze towards him. He refused to look at the man who just allowed his crew to openly slaughter a bunch of merchants, refused to look at the man who didn’t let him help those poor men, who he knew had wives and kids that would never see them again.

  
“I must admit, your stubbornness is one of your less attractive traits.” Minho growled at Thomas’s words and was half tempted to grab the nearest blunt object and beat the pirate down with it. His arms were free to do so, yet irrationality wasn’t going to get him anywhere. _Yet._ They were far away from any land, after all.

  
“Aww c’mon, _Princey._ Let’s talk.”

  
“Fuck off,” Minho spoke bluntly, his eyes narrow as he glared at the young captain, not that it seemed to phase him. If anything, he seemed delighted, “I don’t want to talk to a cold-blooded, heartless scoundrel of the sea who murders innocent men for fun.”

  
A chuckle slid from Thomas as he slid his hand under Minho’s chin and tilted it upwards.

  
“By all means, keep insulting me,” he purred as he held the prince firmly in place, “I’m enjoying it.”

  
A sound of hateful disgust came from Minho as he knocked the captain's hand away and moved to leave the room. He had tried to leave multiple times now, but he was always dragged back to that godforsaken bed and it appeared now was no different than those previous attempts. The feeling of a hand on his wrist and then he was pulled back down, only this time his hands were being held above his head.

  
“Get the fuck off of me, you bastard.”

  
“You’ve got such a sailor’s mouth for such a pretty face,” Thomas smirked at the bitter expression that formed on Minho’s face, which only furthered the prince’s desire to attack the pirate. Especially with his next words, “I like it.”

  
He quickly fell into a silent defiance as he tried prying his wrists from the bruising grip the younger man was holding them in, which apparently only spurred the lawless man to continue his actions. The telltale sign of a hand trailing down his side, with fingers teasing his stomach and v-line immediately made Minho pick up on the other's intentions and he quickly jerked his knees up – only to start digging them into the other’s chest – in order to defend his dignity. He sure as hell wasn’t going to let the pirate take anything else from him. Not without a fight.

* * *

Thomas left the captain’s quarters particularly smug, which aroused intrigue in The Glade's crew. He approached Newt, wrapped an arm around the blonde’s waist and pressed his chin on the shoulder of his first mate, who simply tilted his head for better access.

  
“You’re happy, Tommy,” Newton chuckled when he heard the content hum come from the dark-haired male, “something to do with the prince you bought onboard?”

  
“I’ve never had this much fun with a prisoner, Newt!” Thomas proclaimed and quickly backed off from the blonde, “he’s so rebellious, he fought against me and hell, the bugger even ignored me. He has such a defiant personality on him, I can’t help but want to aggravate him.”

  
Gally and Frypan sighed heavily. Their captain had always been a peculiar one, and this really wasn’t anything new.

  
“You and your weird preferences, Thomas…” Sigmund huffed disappointedly. He shook his head when he heard Thomas laugh heartily before the captain's mood made a 180 and changed.

  
“I want him as part of the crew, if you’re all okay with that.”

  
“Part of the crew? What the hell for?” Gally raised a thick brow, his blue-grey eyes narrowed in confusion as Thomas leaned back against a gunpowder barrel, a smirk clear on his lips.

  
“For many reasons, Gally. For one, he’d fit right in with you all, what with his temper and attitude. For two, that prince knows how to fight. Properly and dirty, just like us.”

  
Ben let out a grunt of agreement. He had first-hand experience with the prince's methods for fighting and if Thomas hadn’t interrupted when he did, he’d of been a goner for sure.

  
“Besides, I get the feeling he’s more intelligent then he lets on.”

* * *

Minho let out a hiss of pain as he pushed himself up from the sheets. He was in so much pain but he’d refused to let it stop him. He glanced up at the rope ties around his wrists, the ones Thomas had pulled against his skin as he left his mark on the young man, and gave them an experimental tug. Lots of resistance, very tight, but not too strong. The knot that Thomas had done made up for the lack of strength in the woven bindings.

  
Minho gently sat himself up, wary of his hips and ass as he gave another tug while he propped himself on his legs. He glanced out the nearest window, finding no sign of Thomas or the crew. They were probably below deck. _Perfect._

  
The prince leaned forward, his head just above the pillow as he hooked his index finger around the thin black rope around his neck and pulled his necklace out from under his shirt. As soon as he felt the familiar coolness of the shark tooth he always wore, he immediately grasped the object and tore the necklace off his neck, breaking the rope with a clear snap. He angled his wrist slightly and started to cut the rope with his makeshift saw; his eyes would dart from the moving tooth to the window as he heard the rope slowly snap layer by layer.

  
As soon as he reached the last layer, Minho jerked his wrists upwards and severed the final thread. He quickly shoved the rope off his skin and tied the necklace back onto his neck, quietly hurrying out of the room. They were nowhere near a port, yes, but that didn’t mean Minho was going to remain in that accursed cabin. He looked around the deck, finding nothing of use, before he went to the stern of the ship. He wasn’t staying on this boat, that’s for sure, and if that meant feeding the fish and being lost to the Locker, then so be it.

  
He took a quick breath and looked around yet again – finding the coast was still clear – before he readied himself to leap. Just as he was about to, he felt arms around his waist and hissed as an unfortunately familiar chuckle entered his ears.

* * *

Thomas had to admit, he wasn’t anticipating it at all. He had just finished the discussion with his crew, who had all agreed that they’ll allow the royal in the crew, and was heading upstairs to present the offer to the feisty prince just as he caught sight of their possible new addition at the stern. He was baffled by the fact that the other man had escaped until he realised what he was doing and quickly rushed over. He laced his arms around the waist of the tanned male and hauled him back from the rail, unable to resist the temptation to laugh at how unpredictable this older man was.

  
“You really are an interesting one!” Thomas spoke after he heard the harsh sound slip from the figure currently pressed against his chest, “never had someone daring enough to go overboard before.”

  
The crew had come up just in time to hear Thomas’s comment and all of them exchanged equally surprised looks. They all found themselves remaining quiet, refusing to work until the currently one-sided conversation between their captain and captive had finished.

  
“I’d rather be lost to the Locker than be on a ship with a bunch of scoundrels, to be honest with you,” The prince ground out, and quickly pulled away from Thomas as far as he could.

  
Thomas found himself barking out a laugh at the comment from the royal before he hauled him away from the stern and into the center of the hull, though not without difficulty.

  
“I must admit, I wasn’t even expecting to see you loose, but here you are, running wild,” Thomas glanced down at the wrists of the prince, seeing the marks of the rope, but not the rope itself, “how in the seven seas did you manage to get out of those ropes?”

  
Silence. An act of defiance that Thomas had become very familiar with from the future monarch. At first, he couldn’t find anything that the other could have used to escape, but then his eyes landed on the black tied rope around the male’s neck. He hooked a finger under the necklace and followed it down to the dip of the other’s collarbone before he lifted the string up. The moment he did, he promptly caught sight of a very sharp, and very well cared for, shark tooth attached to the material.

  
Thomas huffed a disbelieving laugh.

  
“A fucking _shark tooth_,” he couldn’t believe it and he heard a sound from one of the crew that showed they were just as surprised by Thomas’s discovery, “you are good, Princey.”

  
Thomas soon pulled the necklace off and looked at Newt, who he soon threw the tooth to. The blonde quickly pocketed it, rather surprised by the current situation. Thomas wasn’t wrong about the prince being smarter than he let on, it seemed.

  
The crew watched as their captain double-checked the rest of the tanned male, to ensure there was nothing else he could use, before he started dragging the male below deck with a sharp order for the crew to “stop standing there like a bunch of idiots and get back to work”. They all quickly went to their posts as the dark hair of their captain disappeared beneath the deck.

  
Thomas pulled the prince alongside himself so he could keep an eye on his impulsive detainee. He couldn’t help but smirk as he walked on, he was enjoying the way this man was so deceptive and wild, just like the ocean around them, far too much. He could tell there would never be a dull moment when the older male was part of the crew, and he was quite frankly anticipating those days. However, until then, he supposed he should keep his prince in confinement. He’d convince the prince to be a Glader soon.

* * *

Minho simply watched as the iron door shut in front of him, keeping a close eye on where Thomas was retrieving and returning the cell key. He turned away the moment the pirate looked up and ignored the entertained snicker that came from him. Minho patiently waited for the captain to leave before he leaned against the cool metal and let out a groan he had held in for much too long.

  
He finally let his body cave in and slid down the door to the floor, a gentle thud hitting his eardrums as he landed on the planks beneath him. He pulled his knees upwards, rested his arms atop them and buried his face in his forearms. Any desire to attempt escape had hurriedly left him the moment he saw Thomas chuck his necklace to one of the blonde crew members.

  
A sullen laugh came from him as he realised the gravity of the situation he had been thrust in. Here he was, a man of royal blood, being held on a pirate’s ship after he heard and saw his entire crew slaughtered before him, with a captain who was infamous for his libido and attitude who was sadly interested in Minho. He lifted his head up and pressed the back of his skull onto the welded metal behind him.

  
_Gods, he was so screwed._

**Notes for the Chapter:**

> Failed to post this chapter a lot, but it's thankfully up now!
> 
> This is the only story I can really get any ideas for, but I'll get to the others soon! (Hopefully.)
> 
> Anyways, kudos and comments are always appreciated. Let's me know if you like the story.

**Author's Note:**

> Last I checked, there isn't a pirate AU of The Maze Runner, and I just had to do one! I love the idea of Thomas being the flirtatious pirate captain and Minho being the badass prince.
> 
> Lots of research went into this. Primarily regarding the swords used and ship components.
> 
> And yes, back then silk, tailored or rich clothes were valuable items, hence why Thomas was eyeing up Minho's clothing.
> 
> Anyways! Ending on a kind of sad note, hope you enjoyed the first chapter of Aye, Captain.
> 
> Comments and kudos are not required, but always appreciated!


End file.
